X-111708012-CTCT-C

Variant names:

• chrX-111708012-CTCT-C
• rs761649769
• NM_001099922.3:c.384-10_384-8delCTT

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001099922.3(ALG13):​c.384-10_384-8delCTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 1,078,609 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.000011 (0 hom. 1 hem.)
• Consequence: ALG13 NM_001099922.3 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.35
• Publications: 0 publications found

Genes affected

ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ALG13-AS1 (HGNC:41277): (ALG13 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant X-111708012-CTCT-C is Benign according to our data. Variant chrX-111708012-CTCT-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2732487.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099922.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALG13	NM_001099922.3	MANE Select	c.384-10_384-8delCTT		splice_region intron	N/A	NP_001093392.1	Q9NP73-1
	ALG13	NM_001257231.2		c.150-10_150-8delCTT		splice_region intron	N/A	NP_001244160.1	Q9NP73-3
	ALG13	NM_001324292.2		c.384-10_384-8delCTT		splice_region intron	N/A	NP_001311221.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALG13	ENST00000394780.8	TSL:2 MANE Select	c.384-14_384-12delTCT		intron	N/A	ENSP00000378260.3	Q9NP73-1
	ALG13	ENST00000927365.1		c.384-14_384-12delTCT		intron	N/A	ENSP00000597424.1
	ALG13	ENST00000927366.1		c.384-14_384-12delTCT		intron	N/A	ENSP00000597425.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD2 exomes AF: 0.00000645 AC: 1 AN: 155012 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000146

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000111 AC: 12 AN: 1078609 Hom.: 0 AF XY: 0.00000286 AC XY: 1 AN XY: 349071

African (AFR) AF: 0.00 AC: 0 AN: 25864

American (AMR) AF: 0.00 AC: 0 AN: 33434

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18381

East Asian (EAS) AF: 0.00 AC: 0 AN: 29917

South Asian (SAS) AF: 0.00 AC: 0 AN: 51256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3814

European-Non Finnish (NFE) AF: 0.0000144 AC: 12 AN: 831262

Other (OTH) AF: 0.00 AC: 0 AN: 45129

GnomAD4 genome Cov.: 22

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Developmental and epileptic encephalopathy, 36 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs761649769; hg19: chrX-110951240;